MetaX: A peptide centric metaproteomic data analysis platform using Operational Taxa-Functions (OTF)
Metaproteomics analyzes the functional dynamics of microbial communities by identifying peptides and mapping them to the most likely proteins and taxa. The challenge in this field lies in seamlessly integrating taxonomic and functional annotations to accurately represent the contributions of individual microbial taxa to functional diversity. We introduce MetaX, a comprehensive tool for analyzing taxa-function relationships in metaproteomics by mapping peptides to their lowest common ancestors and assigning functions based on proportional thresholds, ensuring accurate peptide-level mappings. Importantly, MetaX introduces the Operational Taxa-Functions (OTF), a new conceptual unit for exploring microbial roles and interactions within ecosystems. Additionally, MetaX extends traditional taxonomic classification by adding a genome level below the species level, enhancing the accuracy of function attribution to specific genomes. We demonstrated MetaX by reanalyzing metaproteomic data from gu